/*
 * EmpiricalFitnessFunction.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.simulator.fitnessfunctions;


import dr.simulator.random.Random;

public class EmpiricalFitnessFunction extends AbstractFitnessFunction {

	public EmpiricalFitnessFunction(int genomeLength, double[] mutationFitnesses, int stateSize, boolean isRandom) {

		double[][] logFitnessTable = new double[genomeLength][stateSize];

		int index = 0;
		for (int i = 0; i < genomeLength; i++) {
			logFitnessTable[i][0] = 0.0;
			for (int j = 1; j < stateSize; j++) {
				if (isRandom) {
					logFitnessTable[i][j] = Math.log(mutationFitnesses[Random.nextInt(mutationFitnesses.length)]);
				} else {
					logFitnessTable[i][j] = Math.log(mutationFitnesses[index]);
					index = (index + 1) % mutationFitnesses.length;
				}
			}
		}

        setLogFitnessTable(logFitnessTable);
	}
}